Abort on BSkernel calculation: Using screening with less G than Weh interaction yambo

[Shixuan]

Dear users and developers,

I'm a freshman in Yambo and I am trying to complete Bethe-Salpeter kernel runlevel test in WS2 system. After convert single-electron wavefunction from PWSCF format (Pseudopotential: ONCV with fully-relativistic) to Yambo format and finish static screening calculation, there are some warring terms occur in Bethe-Salpeter kernel runlevel and then calculation stop. You can see errors as follows:

*****************************************************************
[WARNING] Using screening with less G than Weh interaction

[WARNING]Missing all or part of PP/Em1s DB

[WARNING]Bethe Salpter section skipped. Impossible to build the kernel.

[07] Timing Overview
*****************************************************************

And the input/output files of static screening calculation and Bethe-Salpeter kernel runlevel are shown as attached files.

All the best,
Shixuan

Department of PHY,
City University of Hong Kong,
Hong Kong SAR

[Shixuan]

Dear all,

Thank you for your patience and I believe that must be some of you guys try to reproduce and solve this problem but also find nothing. Just because this is a problem "not that smart". The output data of static screening was put in a wrong file such that yambo cannot find it. Now I have complete the BSkernel computing by changing the file.

Aoplogize for my careless and hope find you all well!

All the best,
Shixuan
Departmet of PHY,
City University of Hong Kong,
Hong Kong, SAR

[Daniele Varsano]

Dear Shixuan,

great, you solved the problem.

Please note, you can use the -J option, e.g.

Code: Select all

yambo -F input -J Screen

in this way, Yambo search for the needed database in the SAVE and Screen directory.

Best,
Daniele

[Sam-2025]

Dear Dr. Daniele Varsano,

I am following the BSE tutorial as in the following link :
using Yambo 5.3, the first step went well but the kernel step gives the following error. Could you please guide me what is wrong with it, I am exactly following the tutorial and started with the dataset in the tutorial. I attached the input and output file for your consideration.

Also,, when I am ignoring this errors and continuing until the final step, it gave the optical spectrum as a flat line (zero) .

<---> [01] MPI/OPENMP structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] Reciprocal space
<---> [02.04] K-grid lattice
<---> Grid dimensions : 6 6 2
<---> [02.05] Energies & Occupations
<---> [03] Transferred momenta grid and indexing
<---> [BZ sampling] Q-grid is User defined and/or read from the database
<---> [03.01] X + BSE indexes
<---> X + BSE [eval] |########################################| [100%] --(E) --(X)
<---> X + BSE[REDUX] |########################################| [100%] --(E) --(X)
<---> [03.01.01] Sigma indexes
<---> Sigma [eval] |########################################| [100%] --(E) --(X)
<---> Sigma[REDUX] |########################################| [100%] --(E) --(X)
<---> [WARNING] [BS] User bands 6-10 break level degeneracy
<---> [04] Dipoles
<---> [04.01] Setup: observables and procedures
<---> [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
<---> [WARNING] In case H contains other non local terms, these are neglected
<---> [05] Bethe Salpeter Equation driver
<---> [05.01] Bethe Salpeter Equation @q1
<---> [05.01.01] Transition pre-analysis @q1
<---> [05.01.02] Transition Groups build-up @q1
<---> [BSK] Size (resonant): 432
<---> [BSK] (total): 432
<---> [BSK] N. of matrices : 1
<---> [05.01.03] Loading Dipoles @q1
<---> BSE dipoles |########################################| [100%] --(E) --(X)
<---> [05.01.04] Independent Particles properties @q1
<---> IP properties |########################################| [100%] --(E) --(X)
<---> EPS via KK, poles at w>0 reflected also in w<0
<---> [WARNING] [EPS_extend] Possible inaccuracy in the EPS prolungation
<---> [05.01.05] BSE Kernel @q1 (Resonant CORRRELATION EXCHANGE)
<---> [05.01.05.01] Screened interaction header I/O
<---> [05.01.05.02] Main kernel loop
<---> Kernel exch |########################################| [100%] --(E) --(X)
<---> [FFT-BSK-3] Mesh size: 12 12 27
<---> [05.01.05.03] Wave-Function Phases
<---> Kernel corr | | [000%] --(E) --(X)[vacc-login2:183623] *** Process received signal ***
[vacc-login2:183623] Signal: Segmentation fault (11)
[vacc-login2:183623] Signal code: Address not mapped (1)
[vacc-login2:183623] Failing at address: 0x101d64a0
[vacc-login2:183623] [ 0] /lib64/libc.so.6(+0x3e6f0)[0x7f4545c3e6f0]
[vacc-login2:183623] [ 1] yambo[0x545170]
[vacc-login2:183623] [ 2] yambo[0x53a2a5]
[vacc-login2:183623] [ 3] yambo[0x418f76]
[vacc-login2:183623] [ 4] yambo[0x41c72c]
[vacc-login2:183623] [ 5] yambo[0x41209f]
[vacc-login2:183623] [ 6] yambo[0x40b1e5]
[vacc-login2:183623] [ 7] yambo[0x409f46]
[vacc-login2:183623] [ 8] yambo[0x6e06a1]
[vacc-login2:183623] [ 9] yambo[0x4082f6]
[vacc-login2:183623] [10] /lib64/libc.so.6(+0x29590)[0x7f4545c29590]
[vacc-login2:183623] [11] /lib64/libc.so.6(__libc_start_main+0x80)[0x7f4545c29640]
[vacc-login2:183623] [12] yambo[0x408385]
[vacc-login2:183623] *** End of error message ***
Segmentation fault (core dumped)

[Daniele Varsano]

Dear Samira,

I do not what is going wrong here.
Can you try to run all the flow in a single run from scratch?
1. remove your 3D-BSE directory
2. generate input file:
> yambo -X s -o b -k sex -y d -F bse.in
3. edit the input file, setting the parameters as in the tutorial (both screening and bse)
4. Run:
> yambo -F bse.in

If it fails please report relevant files.

Best,
Daniele

[Sam-2025]

Dear Dr. Daniele Varsano,
Thank you so much for your guidance. I followed your suggestion. But it is giving the same error. the out put and input file attached for your consinderation. Could you please look at them. Thank you so much.
I am using the hBN dataset that is attached in website and has SAVE folder.


<---> [01] MPI/OPENMP structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] Reciprocal space
<---> [02.04] K-grid lattice
<---> Grid dimensions : 6 6 2
<---> [02.05] Energies & Occupations
<---> [03] Transferred momenta grid and indexing
<---> [BZ sampling] Q-grid is User defined and/or read from the database
<---> [03.01] X + BSE indexes
<---> X + BSE [eval] |########################################| [100%] --(E) --(X)
<---> X + BSE[REDUX] |########################################| [100%] --(E) --(X)
<---> [03.01.01] Sigma indexes
<---> Sigma [eval] |########################################| [100%] --(E) --(X)
<---> Sigma[REDUX] |########################################| [100%] --(E) --(X)
<---> [WARNING] [Xs] User bands 1-40 break level degeneracy
<---> [WARNING] [BS] User bands 6-10 break level degeneracy
<---> [04] Dipoles
<---> [04.01] Setup: observables and procedures
<---> [DIP] Database not correct or missing. To be computed
<---> [x,Vnl] computed using 4 projectors
<---> R V P [g-space] |########################################| [100%] --(E) --(X)
<---> [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
<---> [WARNING] In case H contains other non local terms, these are neglected
<---> [05] Static Dielectric Matrix
<---> [LA] SERIAL linear algebra
<---> [FFT-X] Mesh size: 12 12 27
<---> [X-CG] R(p) Tot o/o(of R): 1933 18432 100
<---> [X] Upper matrix triangle filled
<---> Xo@q[1] |########################################| [100%] --(E) --(X)
<---> X@q[1] |########################################| [100%] --(E) --(X)
<---> [X-CG] R(p) Tot o/o(of R): 1581 18432 100
<---> Xo@q[2] |########################################| [100%] --(E) --(X)
<---> X@q[2] |########################################| [100%] --(E) --(X)
<---> [X-CG] R(p) Tot o/o(of R): 5861 18432 100
<02s> Xo@q[3] |########################################| [100%] --(E) --(X)
<02s> X@q[3] |########################################| [100%] --(E) --(X)
<02s> [X-CG] R(p) Tot o/o(of R): 4775 18432 100
<02s> Xo@q[4] |########################################| [100%] --(E) --(X)
<02s> X@q[4] |########################################| [100%] --(E) --(X)
<02s> [X-CG] R(p) Tot o/o(of R): 4948 18432 100
<03s> Xo@q[5] |########################################| [100%] --(E) --(X)
<03s> X@q[5] |########################################| [100%] --(E) --(X)
<03s> [X-CG] R(p) Tot o/o(of R): 4034 18432 100
<03s> Xo@q[6] |########################################| [100%] --(E) --(X)
<03s> X@q[6] |########################################| [100%] --(E) --(X)
<03s> [X-CG] R(p) Tot o/o(of R): 3704 18432 100
<04s> Xo@q[7] |########################################| [100%] --(E) --(X)
<04s> X@q[7] |########################################| [100%] --(E) --(X)
<04s> [X-CG] R(p) Tot o/o(of R): 3050 18432 100
<05s> Xo@q[8] |########################################| [100%] --(E) --(X)
<05s> X@q[8] |########################################| [100%] --(E) --(X)
<05s> [X-CG] R(p) Tot o/o(of R): 4770 18432 100
<05s> Xo@q[9] |########################################| [100%] --(E) --(X)
<05s> X@q[9] |########################################| [100%] --(E) --(X)
<05s> [X-CG] R(p) Tot o/o(of R): 3948 18432 100
<06s> Xo@q[10] |########################################| [100%] --(E) --(X)
<06s> X@q[10] |########################################| [100%] --(E) --(X)
<06s> [X-CG] R(p) Tot o/o(of R): 7173 18432 100
<06s> Xo@q[11] |########################################| [100%] --(E) --(X)
<06s> X@q[11] |########################################| [100%] --(E) --(X)
<06s> [X-CG] R(p) Tot o/o(of R): 5885 18432 100
<07s> Xo@q[12] |########################################| [100%] --(E) --(X)
<07s> X@q[12] |########################################| [100%] --(E) --(X)
<07s> [X-CG] R(p) Tot o/o(of R): 2712 18432 100
<08s> Xo@q[13] |########################################| [100%] --(E) --(X)
<08s> X@q[13] |########################################| [100%] --(E) --(X)
<08s> [X-CG] R(p) Tot o/o(of R): 2247 18432 100
<08s> Xo@q[14] |########################################| [100%] --(E) --(X)
<08s> X@q[14] |########################################| [100%] --(E) --(X)
<08s> [06] Bethe Salpeter Equation driver
<08s> [06.01] Bethe Salpeter Equation @q1
<08s> [06.01.01] Transition pre-analysis @q1
<08s> [06.01.02] Transition Groups build-up @q1
<08s> [BSK] Size (resonant): 432
<08s> [BSK] (total): 432
<08s> [BSK] N. of matrices : 1
<08s> [06.01.03] Loading Dipoles @q1
<08s> BSE dipoles |########################################| [100%] --(E) --(X)
<08s> [06.01.04] Independent Particles properties @q1
<08s> IP properties |########################################| [100%] --(E) --(X)
<08s> EPS via KK, poles at w>0 reflected also in w<0
<08s> [WARNING] [EPS_extend] Possible inaccuracy in the EPS prolungation
<08s> [06.01.05] BSE Kernel @q1 (Resonant CORRRELATION EXCHANGE)
<08s> [06.01.05.01] Screened interaction header I/O
<08s> [06.01.05.02] Main kernel loop
<08s> Kernel exch |########################################| [100%] --(E) --(X)
<08s> [FFT-BSK-3] Mesh size: 12 12 27
<08s> [06.01.05.03] Wave-Function Phases
<08s> Kernel corr | | [000%] --(E) --(X)[vacc-login3:2932246] *** Process received signal ***
[vacc-login3:2932246] Signal: Segmentation fault (11)
[vacc-login3:2932246] Signal code: Address not mapped (1)
[vacc-login3:2932246] Failing at address: 0x107b0740
[vacc-login3:2932246] [ 0] /lib64/libc.so.6(+0x3e6f0)[0x7f8d72e3e6f0]
[vacc-login3:2932246] [ 1] yambo[0x545170]
[vacc-login3:2932246] [ 2] yambo[0x53a2a5]
[vacc-login3:2932246] [ 3] yambo[0x418f76]
[vacc-login3:2932246] [ 4] yambo[0x41c72c]
[vacc-login3:2932246] [ 5] yambo[0x41209f]
[vacc-login3:2932246] [ 6] yambo[0x40b1e5]
[vacc-login3:2932246] [ 7] yambo[0x409f46]
[vacc-login3:2932246] [ 8] yambo[0x6e06a1]
[vacc-login3:2932246] [ 9] yambo[0x4082f6]
[vacc-login3:2932246] [10] /lib64/libc.so.6(+0x29590)[0x7f8d72e29590]
[vacc-login3:2932246] [11] /lib64/libc.so.6(__libc_start_main+0x80)[0x7f8d72e29640]
[vacc-login3:2932246] [12] yambo[0x408385]
[vacc-login3:2932246] *** End of error message ***
Segmentation fault (core dumped)

[Sam-2025]

Dear Dr. Daniele Varsano,

We reinstalled Yambo 5.3 and it worked — I was able to successfully complete the BSE tutorial and obtain the expected results. Thank you very much for your guidance and support.

However, I’m still encountering issues (attached) when running the exciton–phonon coupling calculations. Despite multiple installations, the problem persists. I’m currently using the older version of Yambo as suggested by Prof. Claudio Attaccalite, but I haven’t been able to reproduce the results shown in the tutorial. I’m not sure whether this is due to a bug in the older version, an installation issue, or perhaps a misunderstanding on my part.

I’m aware that this version has known gauge issues with exciton–phonon coupling, but I’d still like to test it first and deal with the gauge-related corrections afterward.


[ERROR] STOP signal received while in[07.01.05.03] Main kernel loop
[ERROR] Writing File ./SAVE//ndb.BS_Q1_CPU_0; Variable L_kind; NetCDF: Attempt to convert between text & numbers